[gmx-users] simulation single molecule in water

[Emanuel Birru]

It would be better if you run it a bit longer than 10ns and check the density again. But it is not a big problem I guess as the density of water at 300K should not be exactly 1000kg/m^3. Its ~1000kg/m^3 at 277K. do not expect to get exactly real value :) Additionally your system is not purely water molecules in a box there is a small molecule in it which might have an effect on the density.

Cheers,

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Souilem Safa
Sent: Tuesday, 7 May 2013 4:38 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] simulation single molecule in water

Dear gromacs users,
I'm simulating a single molecule in spc water. I'm using a cubic water box which has 3.4 nm size.
I got the toplogy of my molecule via PRODRG.
After running minimization, NVT , NPT and MD for 10 ns , I checked the density of water ,it was less than the real value (1000 kg m\S-3\N) ,actually I got around 950.
I have checked my mdp file in the NPT step and I was wondering about tau_p that I should use. First I used 2.0 ps with Parrinello-Rahman coupling.
After checking in gromacs archive, I found it is better to use 0.5 ps, I have changed tau-p ,but I still have density value less than 1000.
Details of my  mdp file are below :
 Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 5000000    ; 2 * 5000000 = 10000 ps, 1 ns
dt        = 0.002        ; 2 fs
; Output control
nstxout        = 1000        ; save coordinates every 2 ps
nstvout        = 1000        ; save velocities every 2 ps
nstxtcout    = 1000        ; xtc compressed trajectory output every 2 ps
nstenergy    = 1000        ; save energies every 2 ps
nstlog        = 1000        ; update log file every 2 ps
; Bond parameters
continuation    = yes        ; Restarting after NPT
constraint_algorithm = lincs    ; holonomic constraints
constraints    = all-bonds    ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter    = 1        ; accuracy of LINCS
lincs_order    = 4        ; also related to accuracy
; Neighborsearching
ns_type        = grid        ; search neighboring grid cells
nstlist        = 5        ; 10 fs
rlist        = 1.0        ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.0        ; short-range electrostatic cutoff (in nm)
rvdw        = 1.0        ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype    = PME        ; Particle Mesh Ewald for long-range
electrostatics
pme_order    = 4        ; cubic interpolation
fourierspacing    = 0.16        ; grid spacing for FFT
; Temperature coupling is on
tcoupl        = V-rescale    ; modified Berendsen thermostat
tc-grps        = system    ; two coupling groups - more accurate
tau_t        = 0.1        ; time constant, in ps
ref_t        = 300         ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl        = Parrinello-Rahman    ; Pressure coupling on in NPT
pcoupltype    = isotropic    ; uniform scaling of box vectors
tau_p        = 0.50        ; time constant, in ps
ref_p        = 1.0        ; reference pressure, in bar
compressibility = 4.5e-5    ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc        = xyz        ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel        = no        ; Velocity generation is off

What should be the origin of this density difference?
looking forward to your advise
-- 
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